#87 remove version pins for markupsafe, flask and werkzeug

also remove dependency on flask-api

.github/workflows/pr-checks.yaml

@@ -39,7 +39,6 @@ jobs:
           conda env create -f environment.yml
           eval "$(conda shell.bash hook)"
           conda activate cellxgene-gateway
-          pip install markupsafe==2.0.1 # temporary workaround for jinja2-2.11.3 calling soft_unicode in markupsafe
           python setup.py install
 
       - name: Run tests

Changelog.md

@@ -1,3 +1,8 @@
+# UNRELEASED
+
+* Removed dependency on flask-api enabling update of werkzeug
+* Updated dependencies (python 3.11, numpy 1.26, unpinned flask, werkzeug)
+
 # 0.3.12
 
 * #81 List gene set annotations when cell annotations not present

Dockerfile

@@ -1,7 +1,7 @@
-FROM python:3.9
+FROM python:3.11
 
-RUN pip install --upgrade pip \
-    && pip install cellxgene-gateway 'MarkupSafe<2.1'
+RUN pip install --upgrade pip
+RUN pip install "cellxgene-gateway>=0.4"
 
 ENV CELLXGENE_DATA=/cellxgene-data
 ENV CELLXGENE_LOCATION=/usr/local/bin/cellxgene

README.md

@@ -110,7 +110,7 @@ Additional environment variables can be provided with the `-e` parameter:
 
 ```bash
 docker run -it --rm \
--v <local_data_dir>:/cellxgene-data \
+-v ../cellxgene_data:/cellxgene-data \
 -e GATEWAY_PORT=8080 \
 -p 8080:8080 \
 cellxgene-gateway
@@ -191,6 +191,35 @@ black .
 
 If you need help for any reason, please make a github ticket. One of the contributors should help you out.
 
+# Releasing New Versions
+
+## How to prepare for release
+
+- Update Changelog.md and version number in __init__.py
+- Cut a release on github
+	- Go to your project homepage on GitHub
+	- On right side, you will see [Releases](https://github.com/Novartis/cellxgene-gateway/releases) link. Click on it.
+	- Click on Draft a new release
+	- Fill in all the details
+		- Tag version should be the version number of your package release
+		- Release Title can be anything you want, but we use v0.3.11 (the same as the tag to be created on publish)
+		- Description should be changelog
+	- Click Publish release at the bottom of the page
+	- Now under Releases you can view all of your releases.
+	- Copy the download link (tar.gz) and save it somewhere
+
+## How to publish to PyPI
+
+Make sure your `.pypirc` is set up for testpypi and pypi index servers.
+
+
+```bash
+rm -rf dist
+python setup.py sdist bdist_wheel
+python -m twine upload --repository testpypi dist/*
+python -m twine upload dist/*
+```
+
 # Contributors
 
 * Niket Patel - https://github.com/NiketPatel9

cellxgene_gateway/backend_cache.py

@@ -11,7 +11,7 @@
 from threading import Thread
 from typing import List
 
-from flask_api import status
+from http import HTTPStatus
 
 from cellxgene_gateway import env
 from cellxgene_gateway.cache_entry import CacheEntry, CacheEntryStatus
@@ -53,7 +53,7 @@ def check_path(self, source, path):
             return matches[0]
         else:
             raise CellxgeneException(
-                status.HTTP_500_INTERNAL_SERVER_ERROR,
+                HTTPStatus.INTERNAL_SERVER_ERROR,
                 "Found " + str(len(matches)) + " for " + path,
             )
 
@@ -71,7 +71,7 @@ def check_entry(self, key):
             return matches[0]
         else:
             raise CellxgeneException(
-                status.HTTP_500_INTERNAL_SERVER_ERROR,
+                HTTPStatus.INTERNAL_SERVER_ERROR,
                 "Found " + str(len(matches)) + " for " + key.dataset,
             )
 

cellxgene_gateway/dir_util.py

@@ -9,8 +9,6 @@
 
 import os
 
-from flask_api import status
-
 from cellxgene_gateway import env
 from cellxgene_gateway.cellxgene_exception import CellxgeneException
 

cellxgene_gateway/subprocess_backend.py

@@ -10,7 +10,7 @@
 import logging
 import subprocess
 
-from flask_api import status
+from http import HTTPStatus
 
 from cellxgene_gateway.cache_entry import CacheEntryStatus
 from cellxgene_gateway.dir_util import make_annotations
@@ -76,10 +76,10 @@ def launch(self, cellxgene_loc, scripts, cache_entry):
                     or "Could not open file" in stderr
                 ):
                     message = "File was invalid."
-                    http_status = status.HTTP_400_BAD_REQUEST
+                    http_status = HTTPStatus.BAD_REQUEST
                 else:
                     message = "Cellxgene failed to launch dataset."
-                    http_status = status.HTTP_500_INTERNAL_SERVER_ERROR
+                    http_status = HTTPStatus.INTERNAL_SERVER_ERROR
 
                 cache_entry.status = CacheEntryStatus.error
                 cache_entry.set_error(message, stderr, http_status)

environment.yml

@@ -2,9 +2,9 @@ name: cellxgene-gateway
 channels:
 - conda-forge
 dependencies:
-- python=3.9
+- python=3.11
 - requests
-- flask==2.2.5
+- flask
 - psutil
 - black
 - twine
@@ -13,6 +13,5 @@ dependencies:
 - pip
 - pip:
   - pre_commit
-  - flask-api
-  - werkzeug==2.3.8
+  - werkzeug
   - cellxgene

requirements.txt

@@ -1,6 +1,5 @@
 cellxgene
-flask==2.2.5
-flask-api
-werkzeug==2.3.8
+flask
+werkzeug
 psutil
 requests